Animating for interchangeable model parts?
My first instinct is to use a single armature, and have different meshes with an armature modifier pointing to the same armature.  In simple cases you could instead parent the mesh to one bone in the armature.  In more complicated cases you can use the armature modifier and vertex groups with weights to have the mesh modified by the appropriate subset of bones.

How exactly that translates to Unity, I am not sure.